LifeWatch - EGI Competence Centre EGI Community Forum Bari 2015 - PowerPoint PPT Presentation

LifeWatch - EGI Competence Centre EGI Community Forum – Bari 2015 Observatories: VREs and Data portals LifewatchGreece Portal : Semantic web with Data services, Parallelizing R with RvLab, Manipulating specimens with MicroCT By Emmanouela Panteri Contributors :N.Minadakis,Y.Marketakis, C.Bekiari, M.Doerr, A.Gougousis, A.Oulas, K.Keklikoglou, I.Filiopoulou, N.Michalakis, C.Arvanitidis 11/11/2015 1

LifeWatch Greece e-infrastructure LWG e-infrastructure: ● Multi-server e-infrastructure currently deployed in HCMR, Crete ● Hosts biodiversity data and applications Applications: ● e-services : searching datasets/ data or one-shot analyses ● vLabs : interfaces for advanced selection of datasets/data, and more elaborated suites of analyses 11/11/2015 2

Accessed by: LifeWatch Greece Portal https://portal.lifewatchgreece.eu/ 11/11/2015 3

Accessed by: LifeWatch Greece Portal https://portal.lifewatchgreece.eu/ 11/11/2015 4

LifeWatch Greece Portal vLabs Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT 11/11/2015 5

The Problem Main characteristics of biodiversity data: ● its cross-disciplinary character . ● Extremely broad range of data types and structures.(xls, csv, DwC Archives etc) ● Broad variety of semantic concepts which encompasses. ● It remains widely distributed and unconnected . http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 6

The goal Our goal in the context of LWGreece: ● Support cataloguing and publishing of all the relevant meta- data information of the Greek biodiversity domain. ● Integrate data from heterogeneous sources by supporting the definitions of appropriate models. ● Efficiently discover biodiversity data of interest and provide replies to complex queries that could not be answered from the individual sources. http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 7

The idea Exploit the events’ information that is explicitly or implicitly contained in the datasets, model the different concepts and entities of the biodiversity domain and take advantage of the semantic graph ’s capabilities to navigate efficiently through the different contents and discover data of interest . http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 8

Design and implementation 3 Components Architecture: 1) Directory Service 2) Metadata Repository 3) Content Storage More than 20 Web Services. 1) Publishing Metadata/Data 2) Searching Metadata 3) Discovering Data 4) Browsing Services 5) Mapping Services 6) Transforming Metadata 7) Annotation Services http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 9

Search Data http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 10

Publish data http://metacatalogue.portal.lifewatchgreece.eu/ 11/11/2015 11

LifeWatch Greece Portal vLabs Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT 11/11/2015 12

R Virtual-LABoratory basics ● Ecological/biological interest ● Offer statistical and visualization tools for LifeWatch ESFRI, using R statistical language. Main Objective: ● Optimize certain VEGAN package functions (Community Ecology Package), which supports, clustering and ordination methods, diversity analysis and other functions for community and vegetation ecologists. More specific issues addressed are: ● Big data manipulation (overcome memory barriers) ● Computational time speed-up (task segmentation multi-cores, cluster computing environment at HCMR – recently upgraded from LlifeWatch) ● Develop an efficient and friendly user interface for analysis of ecological community data. http://rvlab.portal.lifewatchgreece.eu/ 11/11/2015 13

RvLAB file types http://rvlab.portal.lifewatchgreece.eu/ 11/11/2015 14

RvLAB main page http://rvlab.portal.lifewatchgreece.eu/ 11/11/2015 15

RvLAB main page Workspace area Functions area Submitted Jobs area http://rvlab.portal.lifewatchgreece.eu/ 11/11/2015 16

RvLAB functions http://rvlab.portal.lifewatchgreece.eu/ 11/11/2015 17

RvLAB Jobs 11/11/2015 18

RvLAB Jobs results Jobs Results 11/11/2015 19

LifeWatch Greece Portal vLabs Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT 11/11/2015 20

Micro-Computed Tomography Exterior parts MicroCT offers: ● Collection of virtual galleries of scanned taxa, displayed and disseminated ● Manipulation of the 3D models through a series of online tools ● Ability to download the datasets for local Interior parts manipulations 11/11/2015 21

MicroCT main page MicroCT main page Specimen Details http://microct.portal.lifewatchgreece.eu/ 11/11/2015 22

MicroCT offers Medadata Visualisation Video 11/11/2015 23

LifewatchGreece Mobile Applications 11/11/2015 24

Mobile Applications Citizen Science MicroCT RvLab medOBIS 11/11/2015 25

RvLab Mobile app workflow 11/11/2015 26

MicroCT vlab Mobile app workflow 11/11/2015 27

Thank you 11/11/2015 28